adagrad                 AdaGrad SGD optimization
adam                    Adam SGD optimization
adamW                   AdamW SGD optimization
adaptive_gd             Adaptive gradient descent
ar                      ngme AR(p) model specification
ar1                     ngme AR(1) model specification
argo_float              Argo float dataset
arma                    ngme ARMA(p, q) model specification
arma11                  Convenience wrapper for ARMA(1,1)
batch_decay             Batch/checkpoint decay helper
batch_means_ci          Pooled Batch-Means Confidence Intervals from
                        Multiple Chains
batch_means_estimator   Batch-Means Covariance Estimator for SGD
                        Trajectories
bfgs                    BFGS optimization
bv                      Ngme bivariate model specification
bv_matern               Ngme bivariate model with Matern sub_models
calibrate_inv_exp_lambda_driven_nig
                        Calibrate Inverse-Exponential Prior for NIG
                        Driven Noise
cienaga                 The swamp of Cienaga Grande in Santa Marta,
                        Colombia
cienaga.border          The x y location of the border of the swamp of
                        Cienaga Grande in Santa Marta, Colombia
compare_noise_kld       Compare noise objects using Kullback-Leibler
                        divergence
compute_index_corr_from_map
                        Helper function to compute the index_corr
                        vector
compute_log_like        Compute Gaussian log-likelihood
compute_ngme_ci         Refit an Existing ngme Object with SGD and
                        Compute Batch-Means CI
compute_ngme_sgld_samples
                        Refit an Existing ngme Object with SGLD and
                        Extract Samples
compute_score_given_pred
                        Compute the scores given the prediction
control_ngme            Generate control specifications for the ngme
                        model
control_opt             Generate control specifications for 'ngme()'
                        function.
control_opt_batch_ci    Generate CI-focused control settings for
                        batch-means inference
create_paired_cv_splits
                        Create paired indices for bivariate
                        cross-validation Ensures that paired
                        observations (e.g., u_wind and v_wind at same
                        location) are kept together in the same fold
cross_validation        Compute the cross-validation for the ngme model
                        Perform cross-validation for ngme model first
                        into sub_groups (a list of target, and train
                        data)
f                       Specifying a latent process model (wrapper
                        function for each model)
gal                     The Generalized Asymmetric Laplace (GAL)
                        Distribution
generic                 Generic precision matrix operator
generic_ns              Non-stationary precision matrix operator with
                        custom matrix combinations
get_data_from_formula   Extracts design matrix from a formula and data.
get_parameter_distance
                        Calculate parameter distance from true values
get_trace_trajectories
                        Get trace trajectories from ngme fitting
get_trajectories        get the trajectories of parameters of the model
gig                     The Generalised Inverse-Gaussian (GIG)
                        Distribution
ig                      The Inverse-Gaussian (IG) Distribution
igam                    The Inverse-Gamma (IGam) Distribution
iid                     ngme iid model specification
make_time_series_cv_index
                        Create Time Series Cross-Validation Indices
matern                  ngme Matern SPDE model specification
mean_list               taking mean over a list of nested lists
merge_noise             Merge 2 noise into 1 noise
merge_replicates        Merge model of replicates into model of 1
                        replicate given train_idx and test_idx, the
                        merged model contains all the information of
                        train_idx from different replicates.
momentum                Momentum SGD optimization
name2fun                Convert transformation name to function
ngme                    Fit an additive linear mixed effect model over
                        replicates
ngme_as_sparse          Convert sparse matrix into sparse dgCMatrix
ngme_batch_ci           Batch-Means Confidence Intervals from an ngme
                        Fit
ngme_cov_matrix         variance of the data or the latent field
ngme_make_mesh_repls    ngme make mesh for different replicates
ngme_model_types        Show ngme model types
ngme_noise              ngme noise specification
ngme_noise_types        Show ngme noise types
ngme_optimizers         List supported optimizers
ngme_parse_formula      Parse the formula for ngme function
ngme_post_samples       posterior samples of different latent models
ngme_prior_types        Show ngme priors
ngme_result             Access the result of a ngme fitted model
ngme_sgld_ci            Quantile Confidence Intervals from SGLD Samples
ngme_sgld_samples       Extract Posterior-like Samples from Stored SGLD
                        Trajectories
ngme_ts_make_A          Make observation matrix for time series
ngme_update             Check whether a newer stable version of ngme2
                        is available
nig                     The Normal Inverse-Gaussian (NIG) Distribution
noise_moments           Moments of stationary NIG and GAL noise
openmp_test             Test OpenMP availability and report the number
                        of threads.
ou                      Ornstein-Uhlenbeck Process Model
plot.ngme_noise         Plot the density of one or more stationary
                        noise objects
plot.parameter_distance
                        Plot method for parameter_distance
pm25_quarterly_2022     Quarterly PM2.5 monitor averages over CONUS in
                        2022
poly_decay              Polynomial schedule helper
posterior_plot          Plot Posterior Distributions from SGLD Samples
precision_matrix_multivariate
                        Compute the precision matrix for multivariate
                        model
precision_matrix_multivariate_spde
                        Compute the precision matrix for multivariate
                        spde Matern model
precond_sgd             Preconditioner SGD optimization
predict.ngme            Predict function of ngme2 predict using ngme
                        after estimation
print.ngme              Print an ngme model
print.ngme_model        Print ngme model
print.ngme_noise        Print ngme noise
print.ngme_operator     Print ngme operator
print.ngme_replicate    Print ngme object
print.ngme_trajectories
                        Print method for ngme_trajectories
print.noise_kld_comparison
                        Print method for noise_kld_comparison
print.parameter_distance
                        Print method for parameter_distance
prior_half_cauchy       Prior Half-Cauchy
prior_inv_exponential   Prior Inverse-Exponential
prior_none              Prior None
prior_normal            Prior Normal
prior_pc_sd             Prior PC-SD
priors                  Prior Container
re                      ngme random effect model
rmsprop                 Root Mean Square Propagation (RMSProp) SGD
                        optimization
rw1                     Random Walk Model of Order 1 (RW1)
rw2                     Random Walk Model of Order 2 (RW2)
sgd                     Vanilla SGD optimization
sgld                    Stochastic Gradient Langevin Dynamics (SGLD)
                        optimization
simulate.ngme           Simulate from a ngme object (possibly with
                        replicates)
simulate.ngme_model     Simulate latent process with noise
simulate.ngme_noise     Simulate ngme noise object
spacetime               Ngme space-time non-separable model
                        specification
stepsize_control        Unified stepsize control
stepsize_decay          Stepsize decay schedule
stepsize_schedule       Stepsize schedule
summary.ngme            Summary of ngme fit result
summary.ngme_batch_ci   Summary for Batch-Means CI Results
tp                      ngme tensor-product model specification
traceplot               Trace plot of ngme fitting
var1                    ngme VAR(1) bivariate model specification
                        (Cayley re-parameterization)
